From: <ha...@us...> - 2006-08-19 08:40:43
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Revision: 5404 Author: hansonr Date: 2006-08-19 01:37:57 -0700 (Sat, 19 Aug 2006) ViewCVS: http://svn.sourceforge.net/jmol/?rev=5404&view=rev Log Message: ----------- bob200603 10.x.46b 11.0 beta -- explicit that set defaultDirectory (for now) is applet-only, not app -- allows properly for "" in isosurface command when there is a defaultDirectory Modified Paths: -------------- branches/bob200603/Jmol/script_documentation/JmolApplet.jar branches/bob200603/Jmol/script_documentation/cmds.js branches/bob200603/Jmol/script_documentation/examples-11/Jmol.jar branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet.jar branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet0.jar branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet1.jar branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet2.jar branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet3.jar branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet4.jar branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet5.jar branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet6.jar branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet_i18n.jar branches/bob200603/Jmol/script_documentation/examples-11/_index.htm branches/bob200603/Jmol/script_documentation/examples-11/img/poly.jpg branches/bob200603/Jmol/script_documentation/examples-11/jmol-11-beta.zip branches/bob200603/Jmol/script_documentation/examples-11/new.htm branches/bob200603/Jmol/script_documentation/scripts.xls branches/bob200603/Jmol/src/org/jmol/viewer/FileManager.java branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java Added Paths: ----------- branches/bob200603/Jmol/script_documentation/examples-11/build.htm branches/bob200603/Jmol/script_documentation/examples-11/data/1crn-solvent.jvxl branches/bob200603/Jmol/script_documentation/examples-11/data/water-G03W.out branches/bob200603/Jmol/script_documentation/examples-11/data/zircon.xyz branches/bob200603/Jmol/script_documentation/examples-11/img/zircon.jpg branches/bob200603/Jmol/script_documentation/examples-11/zircon.htm branches/bob200603/Jmol/script_documentation/examples-11/zircon.jpg branches/bob200603/Jmol/script_documentation/misc/bob.htm Modified: branches/bob200603/Jmol/script_documentation/JmolApplet.jar =================================================================== (Binary files differ) Modified: branches/bob200603/Jmol/script_documentation/cmds.js =================================================================== --- branches/bob200603/Jmol/script_documentation/cmds.js 2006-08-18 14:10:27 UTC (rev 5403) +++ branches/bob200603/Jmol/script_documentation/cmds.js 2006-08-19 08:37:57 UTC (rev 5404) @@ -1,5 +1,5 @@ //newCmd('command','examples','flags/xrefs','description','sortorder','param1','param2','param3','param4+') -lastupdate='Aug 17, 2006' +lastupdate='Aug 19, 2006' jmolversion='Jmol Version 11.0(beta) 2006/08/15' newCmd('.animation','','*v+11.0 -- adds greatly expanded frame animation control; *v-10.2;anim','Sets selected animation parameters or turns animation on or off. Note that there are four distinct animation types that can be employed using Jmol: (1) files may contain '+'multiple stuctures that are "played" sequencially, *various types may contain vibrational modes that can be animated, *ve in a predefined way. The "animation" command only refers to method (1). ','1|2|4','','') newCmd('','','*v-10.2;','Turns on or off animation.','*10','._on_off{"ON"}','') @@ -345,7 +345,7 @@ newCmd('','','','','*2','','RASMOL') newCmd('.set (files and scripts)','','*v+11.0 -- introduces several new settings; *v-10.2;','The following commands relate to how files and scripts are loaded and how scripts are executed. ','0|1','','') newCmd('','','*v-10.2;','Sets the URL for a proxy server when {#.load~loading} a file or reading a {#.pmesh~} or {#.isosurface~} or when reading a file-based {#.script~}. A proxy server is a server-side application (typically written using PERL, PHP, or ColdFusion) on the same host as the JAR file that can deliver files from other servers on the internet. Jmol appends "?url=" followed by the URL of the requested data file to the indicated proxy server name. NOte that Java security requires that this call be to the same server that hosts the JAR file. ','*1','appletProxy','"URL"') -newCmd('','','*v-10.2;','Sets the default directory to use for reading all files. This will generally be a relative path such as "./data" or "../files". Note that Java security requires that if the applet is run from a hard drive rather than via the internet, all files read must be either in the directory containing the JAR file or in a subdirectory of that directory. If the applet is unsigned and loaded from the internet, then Java security typically requires that all files read are from the host from which the JAR file was read. But see <b>set appletProxy</b>, above.','*2','defaultDirectory','"directory path"') +newCmd('','','*v-10.2;','(APPLET ONLY) Sets the default directory to use for reading all files. This will generally be a relative path such as "./data" or "../files". Note that Java security requires that if the applet is run from a hard drive rather than via the internet, all files read must be either in the directory containing the JAR file or in a subdirectory of that directory. If the applet is unsigned and loaded from the internet, then Java security typically requires that all files read are from the host from which the JAR file was read. But see <b>set appletProxy</b>, above. This flag is applicable only to the Jmol applet, not to the Jmol application.','*2','defaultDirectory','"directory path"') newCmd('','','*v-10.2;','For crystallographic systems, sets the default lattice to be loaded. {{1 1 1}} loads the standard single unit cell (555). {{2 1 1}} loads two unit cells along the <b>i</b> direction, cells 555 and 655. {{2 2 2}} loads a set of eight unit cells; {{3 3 3}} loads a set of 27. This last is probably most useful, because it loads one unit cell surrounded by all 26 cells sharing its 6 faces, 12 edges, and 8 corners.','*3','defaultLattice','{{i j k}}') newCmd('','','*v-10.2;','Sets a script to run after any file is loaded. The script must be in quotations. If the script itself needs quotation marks, then it should be placed in a file and indicated as follows: <b>set defaultLoadScript "script myscript.scr"</b>.','*4','defaultLoadScript','"script"') newCmd('','','*v-10.2;','Enables (ON) or disables (OFF) script queuing. When script queuing is enabled (the default), scripts that are {#.loop~looping} require {#.quit~} or {#.exit~} to be executed in a subsequent script in order to complete.','*5','scriptQueue','._on_off{"ON"}') Modified: branches/bob200603/Jmol/script_documentation/examples-11/Jmol.jar =================================================================== (Binary files differ) Modified: branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet.jar =================================================================== (Binary files differ) Modified: branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet0.jar =================================================================== (Binary files differ) Modified: branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet1.jar =================================================================== (Binary files differ) Modified: branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet2.jar =================================================================== (Binary files differ) Modified: branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet3.jar =================================================================== (Binary files differ) Modified: branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet4.jar =================================================================== (Binary files differ) Modified: branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet5.jar =================================================================== (Binary files differ) Modified: branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet6.jar =================================================================== (Binary files differ) Modified: branches/bob200603/Jmol/script_documentation/examples-11/JmolApplet_i18n.jar =================================================================== (Binary files differ) Modified: branches/bob200603/Jmol/script_documentation/examples-11/_index.htm =================================================================== --- branches/bob200603/Jmol/script_documentation/examples-11/_index.htm 2006-08-18 14:10:27 UTC (rev 5403) +++ branches/bob200603/Jmol/script_documentation/examples-11/_index.htm 2006-08-19 08:37:57 UTC (rev 5404) @@ -18,6 +18,7 @@ addInfo("pmesh","pmesh inline","pmesh.jpg") addInfo("poly","polyhedra","poly.jpg") addInfo("vibrate","reading vibration data","vibrate.jpg") +addInfo("zircon","Molecular Origami of zircon", "zircon.jpg") function getLinks(){ @@ -64,6 +65,7 @@ <h3><a target=_blank href="http://sourceforge.net/projects/jmol/">Jmol</a> Presentations (not necessarily self-guided)</h3> <a href=http://www.stolaf.edu/academics/chemapps/jmol/presentations/bcce19/hansonr-bcce19-ajax.ppt>BCCE19 Ajax for Chemistry</a> <br/>(requires Windows PC/Microsoft PowerPoint with <a href=http://skp.mvps.org/liveweb.htm>LiveWeb</a> add-in) <br/><a href=http://www.stolaf.edu/academics/chemapps/jmol/presentations/confchem2006/jmol-confchem.htm>Spring 2006 ConfChem paper</a> +<br/><a href=http://www.stolaf.edu/academics/chemapps/jmol/presentations/europe2006/molecularVisualization.ppt>August 2006 Cologne/Nijmegen seminar</a> (requires PC/LiveWeb) </td> <td width=405><a id=theAnchor href=new.htm><img border=0 id=theImage src=http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/img/isoesp.jpg></a></td> Added: branches/bob200603/Jmol/script_documentation/examples-11/build.htm =================================================================== --- branches/bob200603/Jmol/script_documentation/examples-11/build.htm (rev 0) +++ branches/bob200603/Jmol/script_documentation/examples-11/build.htm 2006-08-19 08:37:57 UTC (rev 5404) @@ -0,0 +1,42 @@ +<HTML> +<HEAD> +<script type="text/javascript" src="Jmol-11.js"></script> +</HEAD> +<BODY> +<center> +<table> +<tr><td width=260></td><td> + +<script> +jmolInitialize("..","JmolApplet.jar") +jmolApplet(350,'set defaultdirectory "data";load 1crn.pdb;wireframe 0;') +</script> +</br> +<script>jmolLink("console","console")</script> + +</td><td> + +<script>jmolCheckbox("select *;spacefill 20%","spacefill 0","atoms",1)</script> +<p> +<script>jmolCheckbox("select *;wireframe 0.15","wireframe 0","bonds",0)</script> +<p> +<script>jmolCheckbox("select *;set cartoonRockets off;cartoons on;color group","cartoons off","cartoons",0)</script> +<p> +<script>jmolCheckbox("select *;rockets on;color group","rockets off","rockets",0)</script> +<p> +<script>jmolCheckbox("select *;set cartoonRockets on;cartoons on;color group","cartoons off","cartoonRockets",0)</script> +<p> +<script>jmolCheckbox("select *;isosurface SAS solvent 2.0","isosurface SAS off","solvent-excluded surface",0)</script> +<p> +<script>jmolCheckbox('isosurface JVXL file "1crn-solvent.jvxl"',"isosurface JVXL off","solvent-excluded surface (<a target=_blank href=data/1crn-solvent.jvxl>JVXL</a>)",0)</script> +<p> +<script>jmolCheckbox('select *;isosurface opaque',"isosurface translucent","opaque surface",1)</script> +<p> +<script>jmolCheckbox("select 6-9;isosurface SAS solvent","isosurface SAS off","solvent (residues 6-9)",0)</script> + +</td> +</tr> +</table> +</BODY> +</HTML> + \ No newline at end of file Added: branches/bob200603/Jmol/script_documentation/examples-11/data/1crn-solvent.jvxl =================================================================== --- branches/bob200603/Jmol/script_documentation/examples-11/data/1crn-solvent.jvxl (rev 0) +++ branches/bob200603/Jmol/script_documentation/examples-11/data/1crn-solvent.jvxl 2006-08-19 08:37:57 UTC (rev 5404) @@ -0,0 +1,340 @@ +JVXL solvent-excluded surface +range (-4.797, -2.466, -9.122) to (25.984001, 22.887001, 21.53) +-327 -9.065017 -4.660065 -17.238083 +23 2.9083834 0.0 0.0 +23 0.0 2.3955114 0.0 +23 0.0 0.0 2.8961945 +7 7.0 32.214165 26.64325 6.8502574 +6 6.0 32.06298 24.158258 8.197633 +6 6.0 29.640356 24.103456 9.699965 +8 8.0 28.85234 26.125465 10.571129 +6 6.0 34.336323 24.005192 10.085469 +8 8.0 36.535965 24.243298 8.433847 +6 6.0 34.29853 21.818777 11.912834 +7 7.0 28.563211 21.835787 9.949408 +6 6.0 26.184046 21.67327 11.4630785 +6 6.0 26.766083 20.380697 13.94429 +8 8.0 28.332664 18.63648 14.065231 +6 6.0 24.059992 20.240858 9.941849 +8 8.0 25.148478 17.837124 9.308791 +6 6.0 23.59134 21.622246 7.360483 +7 7.0 25.488626 21.242413 15.905825 +6 6.0 25.813662 20.233297 18.49475 +6 6.0 23.185051 19.711733 19.507645 +8 8.0 21.529652 21.369024 19.246862 +6 6.0 27.151587 22.200502 20.203064 +16 16.0 30.018301 23.481737 18.927496 +7 7.0 22.71262 17.52154 20.650928 +6 6.0 20.118025 16.990528 21.557997 +6 6.0 20.133142 16.616362 24.413372 +8 8.0 22.032318 15.677167 25.494295 +6 6.0 19.004976 14.649157 20.186054 +16 16.0 18.589235 15.151826 16.82612 +7 7.0 18.067673 17.211628 25.630358 +6 6.0 17.854134 17.071785 28.368568 +6 6.0 17.551777 14.4942 29.491066 +8 8.0 17.9335 14.208851 31.783304 +6 6.0 15.552445 18.816004 28.997849 +6 6.0 13.866811 18.492859 26.671597 +6 6.0 15.809449 18.526875 24.487072 +7 7.0 16.77132 12.634708 27.960388 +6 6.0 16.389595 10.042006 28.873125 +6 6.0 16.540773 8.269443 26.613014 +8 8.0 16.48975 9.18029 24.420933 +6 6.0 13.87059 9.677287 30.228058 +8 8.0 11.856142 9.86437 28.404474 +7 7.0 16.78266 5.810908 27.13269 +6 6.0 16.84124 3.9362996 25.05399 +6 6.0 14.326014 3.9495275 23.632915 +8 8.0 14.4942 3.8380337 21.249971 +6 6.0 17.398708 1.2793447 26.312546 +6 6.0 20.246525 1.3265877 27.045761 +6 6.0 16.65038 -0.9013994 24.507858 +6 6.0 21.136587 -0.97509867 28.614233 +7 7.0 12.203852 4.085588 24.866907 +6 6.0 9.722641 4.174405 23.53276 +6 6.0 9.66595 6.3853846 21.658152 +8 8.0 8.813683 6.175625 19.545439 +6 6.0 7.549456 4.4484153 25.469728 +6 6.0 5.1324964 5.4631977 24.318888 +6 6.0 7.1015906 1.9501973 26.84923 +7 7.0 10.593804 8.590695 22.56522 +6 6.0 10.578687 10.89805 20.941944 +6 6.0 12.171726 10.444516 18.613804 +8 8.0 11.436623 11.211745 16.523764 +6 6.0 11.3799305 13.18462 22.470736 +7 7.0 14.450736 9.276666 18.90671 +6 6.0 16.055113 8.709747 16.69951 +6 6.0 14.736084 6.8200216 14.883484 +8 8.0 14.887263 7.139385 12.568569 +6 6.0 18.608133 7.596699 17.583902 +6 6.0 20.318335 6.816242 15.399379 +6 6.0 21.214066 8.879823 13.689177 +7 7.0 22.946945 10.527664 15.183949 +6 6.0 24.109127 12.4892 14.065231 +7 7.0 23.695276 13.099582 11.636933 +7 7.0 25.702168 13.836575 15.499534 +7 7.0 13.579572 4.879273 15.958736 +6 6.0 12.28322 2.9933262 14.295778 +6 6.0 10.1705065 4.3709364 12.799115 +8 8.0 9.851142 3.809688 10.501208 +6 6.0 11.164502 0.8730535 15.873699 +8 8.0 13.209187 -0.51400554 17.030212 +7 7.0 8.783446 6.0131087 14.070901 +6 6.0 6.6990795 7.436073 12.757542 +6 6.0 7.761105 9.167062 10.754432 +8 8.0 6.6820717 9.4505205 8.724866 +6 6.0 5.0323405 8.838249 14.641598 +6 6.0 3.4052863 7.0581274 16.270544 +8 8.0 2.9612007 4.9378543 15.429616 +7 7.0 2.634278 8.035115 18.456955 +7 7.0 9.938069 10.389714 11.347806 +6 6.0 11.204186 12.014879 9.552567 +6 6.0 11.912834 10.540893 7.1790695 +8 8.0 11.59536 11.474418 5.0134435 +6 6.0 13.573902 13.216745 10.873485 +6 6.0 14.898602 15.129147 9.227532 +6 6.0 16.829899 14.335463 7.609927 +6 6.0 14.2334175 17.712404 9.416505 +6 6.0 18.065783 16.136372 6.0357847 +6 6.0 15.4504 19.428274 7.832915 +6 6.0 17.273989 18.604355 6.2209787 +7 7.0 13.039111 8.295898 7.538118 +6 6.0 13.853583 6.816242 5.2742257 +6 6.0 11.557566 6.066021 3.6188257 +8 8.0 11.791891 5.9412985 1.2925727 +6 6.0 15.391821 4.542902 6.1227126 +6 6.0 18.056334 5.397058 7.0486784 +8 8.0 18.92183 7.360483 6.27956 +7 7.0 19.124031 3.6963046 8.577467 +7 7.0 9.435403 5.5312285 4.8584857 +6 6.0 7.1469445 4.9113984 3.291903 +6 6.0 6.2285376 7.3151298 1.897285 +8 8.0 5.569023 7.2130847 -0.35715827 +6 6.0 5.0984807 3.6906354 4.9284053 +6 6.0 2.615381 3.45064 3.4128454 +6 6.0 5.9979906 1.0072241 5.6786275 +7 7.0 6.27578 9.424065 3.250329 +6 6.0 5.4613085 11.876928 2.1278317 +6 6.0 6.96742 12.466524 -0.20975961 +8 8.0 6.047124 13.505873 -2.084368 +6 6.0 5.742878 13.925392 4.2329865 +16 16.0 4.835809 17.03399 3.1161582 +7 7.0 9.442962 11.767324 -0.18897262 +6 6.0 11.139936 12.262433 -2.292238 +6 6.0 10.843248 10.506877 -4.5523505 +8 8.0 11.769214 11.151274 -6.6272697 +6 6.0 13.927282 12.296448 -1.3813897 +6 6.0 14.583016 14.526324 0.3892836 +6 6.0 15.021433 16.90738 -1.1621816 +7 7.0 17.408157 16.735415 -2.5265636 +6 6.0 18.022318 18.01476 -4.5939245 +7 7.0 16.36314 19.558666 -5.72965 +7 7.0 20.395815 17.93539 -5.478316 +7 7.0 9.545007 8.335583 -4.1649566 +6 6.0 9.32202 6.4836507 -6.285229 +6 6.0 8.309127 7.5853615 -8.730535 +8 8.0 9.425954 7.095922 -10.746872 +6 6.0 7.9292912 4.1271615 -5.410286 +6 6.0 9.373042 2.2260976 -3.7624452 +6 6.0 7.38316 0.18330343 -3.0878124 +6 6.0 11.582131 1.145174 -5.230762 +7 7.0 6.2908983 9.061237 -8.585026 +6 6.0 5.2761154 10.159168 -10.954742 +6 6.0 6.7519913 12.358809 -11.946849 +8 8.0 6.160507 13.313121 -14.025547 +6 6.0 2.566248 10.896161 -10.340582 +6 6.0 2.3111353 10.760101 -7.5456767 +6 6.0 4.575027 9.337137 -6.440187 +7 7.0 8.6266 13.3169 -10.504988 +6 6.0 10.140271 15.478748 -11.372373 +6 6.0 9.461859 17.916494 -9.977754 +8 8.0 10.459635 19.861023 -10.828131 +7 7.0 7.9009447 17.835236 -8.054012 +6 6.0 7.1185985 20.048105 -6.638608 +6 6.0 9.480757 21.53721 -5.748547 +8 8.0 11.238201 20.327784 -4.767779 +6 6.0 5.654061 19.252531 -4.204641 +8 8.0 3.875828 17.279655 -4.9567513 +6 6.0 4.270781 21.446503 -2.9309652 +7 7.0 9.393829 24.005192 -6.00177 +6 6.0 11.608587 25.53587 -5.0947013 +6 6.0 12.094248 25.006746 -2.3149147 +8 8.0 10.365149 24.681715 -0.72187537 +6 6.0 10.777107 28.287312 -5.5180006 +6 6.0 8.83636 28.143692 -7.551346 +6 6.0 7.4908743 25.637915 -7.201746 +7 7.0 14.603804 25.12769 -1.7404377 +6 6.0 15.333239 24.761084 0.9448631 +6 6.0 14.034996 26.594116 2.6645138 +8 8.0 13.296114 25.855234 4.7999043 +6 6.0 18.232079 25.105011 1.2472193 +6 6.0 19.72874 22.852459 0.11905275 +6 6.0 22.56522 22.997967 0.73888296 +8 8.0 23.46284 24.991629 1.2869035 +8 8.0 23.695276 20.919268 0.5518 +7 7.0 13.628705 28.97706 1.8254755 +6 6.0 12.49865 30.834661 3.6150463 +6 6.0 9.849253 30.114674 4.4408565 +8 8.0 9.03667 30.549314 6.6045933 +6 6.0 12.481642 33.438705 2.354599 +7 7.0 8.399833 28.946827 2.6550653 +6 6.0 5.809018 28.145582 3.3183591 +6 6.0 5.8298054 25.781536 4.998326 +8 8.0 4.3747163 25.554768 6.76144 +6 6.0 4.1649566 27.659922 0.8730535 +6 6.0 3.429853 30.326326 -0.2437747 +6 6.0 1.7064228 26.199163 1.5325679 +6 6.0 1.428633 31.6737 1.4305228 +7 7.0 7.619376 24.120464 4.3709364 +6 6.0 7.899055 21.824448 6.022557 +6 6.0 8.753212 22.570889 8.685182 +8 8.0 7.987872 21.263199 10.482311 +6 6.0 9.520441 19.87614 4.7980146 +16 16.0 8.218419 18.507977 1.9313 +7 7.0 10.219639 24.589117 8.870375 +6 6.0 11.1097 25.515083 11.38749 +6 6.0 8.874154 26.282312 13.0050955 +8 8.0 8.55668 25.363905 15.165053 +6 6.0 13.001316 27.61835 11.017104 +7 7.0 7.2319818 27.971727 12.014879 +6 6.0 5.085253 28.763523 13.59469 +6 6.0 3.1596222 26.70561 14.048225 +8 8.0 1.7895708 26.667816 16.002201 +6 6.0 3.7529964 31.218277 12.49865 +8 8.0 3.144504 30.65325 9.883267 +6 6.0 5.506662 33.52186 12.661165 +7 7.0 3.0632463 24.92549 12.304008 +6 6.0 1.3511542 22.761751 12.579907 +6 6.0 2.125942 21.023205 14.768211 +8 8.0 0.5404617 20.091568 16.14771 +6 6.0 1.4267433 21.219736 10.057122 +6 6.0 -0.38361442 18.98041 10.117595 +6 6.0 -2.9234061 19.5341 10.667504 +6 6.0 0.36471716 16.535105 9.637603 +6 6.0 -4.716757 17.629257 10.720416 +6 6.0 -1.5136707 14.56034 9.743428 +6 6.0 -3.9287407 15.176391 10.261213 +8 8.0 -5.852482 13.335798 10.314126 +7 7.0 4.6676235 20.75675 15.108361 +6 6.0 5.6427226 18.885921 16.91305 +6 6.0 6.8200216 19.851574 19.331898 +8 8.0 7.1167088 18.35869 21.138477 +6 6.0 7.702524 17.202179 15.542998 +8 8.0 9.684847 18.948284 14.785218 +6 6.0 6.6008134 15.730082 13.294224 +7 7.0 7.528669 22.230738 19.352686 +6 6.0 9.012103 23.31166 21.46729 +6 6.0 11.820237 23.135918 20.987299 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+#-------end of jvxl file data------- \ No newline at end of file Added: branches/bob200603/Jmol/script_documentation/examples-11/data/water-G03W.out =================================================================== --- branches/bob200603/Jmol/script_documentation/examples-11/data/water-G03W.out (rev 0) +++ branches/bob200603/Jmol/script_documentation/examples-11/data/water-G03W.out 2006-08-19 08:37:57 UTC (rev 5404) @@ -0,0 +1,605 @@ + Entering Link 1 = C:\G03W\l1.exe PID= 2732. + + Copyright (c) 1988,1990,1992,1993,1995,1998,2003, Gaussian, Inc. + All Rights Reserved. + + This is the Gaussian(R) 03 program. It is based on the + the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), + the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), + the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), + the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), + the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), + the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon + University), and the Gaussian 82(TM) system (copyright 1983, + Carnegie Mellon University). Gaussian is a federally registered + trademark of Gaussian, Inc. + + This software contains proprietary and confidential information, + including trade secrets, belonging to Gaussian, Inc. + + This software is provided under written license and may be + used, copied, transmitted, or stored only in accord with that + written license. + + The following legend is applicable only to US Government + contracts under DFARS: + + RESTRICTED RIGHTS LEGEND + + Use, duplication or disclosure by the US Government is subject + to restrictions as set forth in subparagraph (c)(1)(ii) of the + Rights in Technical Data and Computer Software clause at DFARS + 252.227-7013. + + Gaussian, Inc. + Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA + + The following legend is applicable only to US Government + contracts under FAR: + + RESTRICTED RIGHTS LEGEND + + Use, reproduction and disclosure by the US Government is subject + to restrictions as set forth in subparagraph (c) of the + Commercial Computer Software - Restricted Rights clause at FAR + 52.227-19. + + Gaussian, Inc. + Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA + + + --------------------------------------------------------------- + Warning -- This program may not be used in any manner that + competes with the business of Gaussian, Inc. or will provide + assistance to any competitor of Gaussian, Inc. The licensee + of this program is prohibited from giving any competitor of + Gaussian, Inc. access to this program. By using this program, + the user acknowledges that Gaussian, Inc. is engaged in the + business of creating and licensing software in the field of + computational chemistry and represents and warrants to the + licensee that it is not a competitor of Gaussian, Inc. and that + it will not use this program in any manner prohibited above. + --------------------------------------------------------------- + + + Cite this work as: + Gaussian 03, Revision B.05, + M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, + M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, + K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, + V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, + G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, + R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, + H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, + C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, + A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, + K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, + V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, + O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, + J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, + J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, + I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, + C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, + B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, + Gaussian, Inc., Pittsburgh PA, 2003. + + ********************************************** + Gaussian 03: x86-Win32-G03RevB.05 8-Nov-2003 + 03-Jul-2006 + ********************************************** + %chk=C:\G03W\Scratch\water.chk + %mem=6MW + %nproc=1 + Will use up to 1 processors via shared memory. + Default route: MaxDisk=2000MB + ----------------------------------------------------- + # opt rhf/6-31g(d) geom=connectivity pop=full gfprint + ----------------------------------------------------- + 1/18=20,38=1,57=2/1,3; + 2/9=110,17=6,18=5,40=1/2; + 3/5=1,6=6,7=1,11=1,16=1,24=100,25=1,30=1/1,2,3; + 4/7=1/1; + 5/5=2,38=5/2; + 6/7=3,28=1/1; + 7//1,2,3,16; + 1/18=20/3(1); + 99//99; + 2/9=110/2; + 3/5=1,6=6,7=1,11=1,16=1,25=1,30=1/1,2,3; + 4/5=5,7=1,16=3/1; + 5/5=2,38=5/2; + 7//1,2,3,16; + 1/18=20/3(-5); + 2/9=110/2; + 6/7=3,19=2,28=1/1; + 99/9=1/99; + ------------------- + Title Card Required + ------------------- + Symbolic Z-matrix: + Charge = 0 Multiplicity = 1 + O + H 1 B1 + H 1 B2 2 A1 + Variables: + B1 0.94741 + B2 0.94741 + A1 105.47853 + + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Initialization pass. + ---------------------------- + ! Initial Parameters ! + ! (Angstroms and Degrees) ! + -------------------------- -------------------------- + ! Name Definition Value Derivative Info. ! + -------------------------------------------------------------------------------- + ! R1 R(1,2) 0.9474 estimate D2E/DX2 ! + ! R2 R(1,3) 0.9474 estimate D2E/DX2 ! + ! A1 A(2,1,3) 105.4785 estimate D2E/DX2 ! + -------------------------------------------------------------------------------- + Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 + Number of steps in this run= 20 maximum allowed number of steps= 100. + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 0.000000 0.000000 0.000000 + 2 1 0 0.000000 0.000000 0.947408 + 3 1 0 0.913046 0.000000 -0.252842 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 + 1 O 0.000000 + 2 H 0.947408 0.000000 + 3 H 0.947408 1.508063 0.000000 + Stoichiometry H2O + Framework group C2V[C2(O),SGV(H2)] + Deg. of freedom 2 + Full point group C2V NOp 4 + Largest Abelian subgroup C2V NOp 4 + Largest concise Abelian subgroup C2 NOp 2 + Standard orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 0.000000 0.000000 0.114720 + 2 1 0 0.000000 0.754031 -0.458881 + 3 1 0 0.000000 -0.754031 -0.458881 + --------------------------------------------------------------------- + Rotational constants (GHZ): 858.0772886 440.9843225 291.2861319 + Standard basis: 6-31G(d) (6D, 7F) + AO basis set: + Atom O1 Shell 1 S 6 bf 1 - 1 0.000000000000 0.000000000000 0.216790073062 + 0.5484671660D+04 0.1831074430D-02 + 0.8252349460D+03 0.1395017220D-01 + 0.1880469580D+03 0.6844507810D-01 + 0.5296450000D+02 0.2327143360D+00 + 0.1689757040D+02 0.4701928980D+00 + 0.5799635340D+01 0.3585208530D+00 + Atom O1 Shell 2 SP 3 bf 2 - 5 0.000000000000 0.000000000000 0.216790073062 + 0.1553961625D+02 -0.1107775495D+00 0.7087426823D-01 + 0.3599933586D+01 -0.1480262627D+00 0.3397528391D+00 + 0.1013761750D+01 0.1130767015D+01 0.7271585773D+00 + Atom O1 Shell 3 SP 1 bf 6 - 9 0.000000000000 0.000000000000 0.216790073062 + 0.2700058226D+00 0.1000000000D+01 0.1000000000D+01 + Atom O1 Shell 4 D 1 bf 10 - 15 0.000000000000 0.000000000000 0.216790073062 + 0.8000000000D+00 0.1000000000D+01 + Atom H2 Shell 5 S 3 bf 16 - 16 0.000000000000 1.424912915560 -0.867160292248 + 0.1873113696D+02 0.3349460434D-01 + 0.2825394365D+01 0.2347269535D+00 + 0.6401216923D+00 0.8137573261D+00 + Atom H2 Shell 6 S 1 bf 17 - 17 0.000000000000 1.424912915560 -0.867160292248 + 0.1612777588D+00 0.1000000000D+01 + Atom H3 Shell 7 S 3 bf 18 - 18 0.000000000000 -1.424912915560 -0.867160292248 + 0.1873113696D+02 0.3349460434D-01 + 0.2825394365D+01 0.2347269535D+00 + 0.6401216923D+00 0.8137573261D+00 + Atom H3 Shell 8 S 1 bf 19 - 19 0.000000000000 -1.424912915560 -0.867160292248 + 0.1612777588D+00 0.1000000000D+01 + There are 10 symmetry adapted basis functions of A1 symmetry. + There are 1 symmetry adapted basis functions of A2 symmetry. + There are 3 symmetry adapted basis functions of B1 symmetry. + There are 5 symmetry adapted basis functions of B2 symmetry. + Integral buffers will be 262144 words long. + Raffenetti 1 integral format. + Two-electron integral symmetry is turned on. + 19 basis functions, 36 primitive gaussians, 19 cartesian basis functions + 5 alpha electrons 5 beta electrons + nuclear repulsion energy 9.2877376136 Hartrees. + NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.76D+00 NAtFMM= 60 Big=F + One-electron integrals computed using PRISM. + NBasis= 19 RedAO= T NBF= 10 1 3 5 + NBsUse= 19 1.00D-06 NBFU= 10 1 3 5 + Harris functional with IExCor= 205 diagonalized for initial guess. + ExpMin= 1.61D-01 ExpMax= 5.48D+03 ExpMxC= 8.25D+02 IAcc=1 IRadAn= 1 AccDes= 1.00D-06 + HarFok: IExCor= 205 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 + Initial guess orbital symmetries: + Occupied (A1) (A1) (B2) (A1) (B1) + Virtual (A1) (B2) (B2) (A1) (B1) (A1) (B2) (A1) (A1) (A2) + (B1) (A1) (B2) (A1) + The electronic state of the initial guess is 1-A1. + Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. + Requested convergence on MAX density matrix=1.00D-06. + Requested convergence on energy=1.00D-06. + No special actions if energy rises. + Keep R1 integrals in memory in canonical form, NReq= 470744. + SCF Done: E(RHF) = -76.0107464887 A.U. after 10 cycles + Convg = 0.3628D-08 -V/T = 2.0020 + S**2 = 0.0000 + + ********************************************************************** + + Population analysis using the SCF density. + + ********************************************************************** + + Orbital symmetries: + Occupied (A1) (A1) (B2) (A1) (B1) + Virtual (A1) (B2) (B2) (A1) (B1) (A1) (B2) (A1) (A1) (A2) + (B1) (A1) (B2) (A1) + The electronic state is 1-A1. + Alpha occ. eigenvalues -- -20.55790 -1.34610 -0.71418 -0.57083 -0.49821 + Alpha virt. eigenvalues -- 0.21300 0.30684 1.03156 1.13339 1.16802 + Alpha virt. eigenvalues -- 1.17845 1.38507 1.43126 2.02052 2.03061 + Alpha virt. eigenvalues -- 2.06722 2.63550 2.96562 3.97762 + Molecular Orbital Coefficients + 1 2 3 4 5 + (A1)--O (A1)--O (B2)--O (A1)--O (B1)--O + EIGENVALUES -- -20.55790 -1.34610 -0.71418 -0.57083 -0.49821 + 1 1 O 1S 0.99462 -0.20953 0.00000 -0.07310 0.00000 + 2 2S 0.02117 0.47576 0.00000 0.16367 0.00000 + 3 2PX 0.00000 0.00000 0.00000 0.00000 0.63927 + 4 2PY 0.00000 0.00000 0.50891 0.00000 0.00000 + 5 2PZ -0.00134 -0.09475 0.00000 0.55774 0.00000 + 6 3S 0.00415 0.43535 0.00000 0.32546 0.00000 + 7 3PX 0.00000 0.00000 0.00000 0.00000 0.51183 + 8 3PY 0.00000 0.00000 0.30390 0.00000 0.00000 + 9 3PZ 0.00046 -0.04982 0.00000 0.40482 0.00000 + 10 4XX -0.00394 -0.00104 0.00000 0.01187 0.00000 + 11 4YY -0.00421 0.02692 0.00000 0.00078 0.00000 + 12 4ZZ -0.00409 0.02132 0.00000 -0.04630 0.00000 + 13 4XY 0.00000 0.00000 0.00000 0.00000 0.00000 + 14 4XZ 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0.00000 + 13 4XY 0.00000 0.00000 0.00000 0.00000 0.00000 + 14 4XZ 0.00000 0.00000 0.00000 0.00000 -0.01405 + 15 4YZ 0.00000 0.02320 -0.19897 0.00000 0.00000 + 16 2 H 1S -0.05370 0.04665 0.83944 0.51743 0.00000 + 17 2S -1.05143 1.41317 -0.42119 -0.43648 0.00000 + 18 3 H 1S -0.05370 -0.04665 -0.83944 0.51743 0.00000 + 19 2S -1.05143 -1.41317 0.42119 -0.43648 0.00000 + 11 12 13 14 15 + (A1)--V (B2)--V (A1)--V (A1)--V (A2)--V + EIGENVALUES -- 1.17845 1.38507 1.43126 2.02052 2.03061 + 1 1 O 1S 0.05103 0.00000 -0.08568 0.00748 0.00000 + 2 2S 0.05229 0.00000 -1.44314 0.07851 0.00000 + 3 2PX 0.00000 0.00000 0.00000 0.00000 0.00000 + 4 2PY 0.00000 -1.04028 0.00000 0.00000 0.00000 + 5 2PZ 0.73177 0.00000 0.50121 -0.00285 0.00000 + 6 3S -0.41033 0.00000 3.63707 -0.23400 0.00000 + 7 3PX 0.00000 0.00000 0.00000 0.00000 0.00000 + 8 3PY 0.00000 1.54088 0.00000 0.00000 0.00000 + 9 3PZ -0.31552 0.00000 -1.15864 0.13057 0.00000 + 10 4XX -0.08033 0.00000 -0.29280 -0.38487 0.00000 + 11 4YY 0.24938 0.00000 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0.01828 0.00000 -1.54919 + 13 4XY 0.00000 0.00000 0.00000 0.00000 + 14 4XZ 0.99932 0.00000 0.00000 0.00000 + 15 4YZ 0.00000 0.00000 1.29538 0.00000 + 16 2 H 1S 0.00000 -0.85893 0.97620 0.13672 + 17 2S 0.00000 -0.14715 -0.02533 -0.55555 + 18 3 H 1S 0.00000 -0.85893 -0.97620 0.13672 + 19 2S 0.00000 -0.14715 0.02533 -0.55555 + DENSITY MATRIX. + 1 2 3 4 5 + 1 1 O 1S 2.07704 + 2 2S -0.18118 0.50716 + 3 2PX 0.00000 0.00000 0.81733 + 4 2PY 0.00000 0.00000 0.00000 0.51798 + 5 2PZ -0.04450 0.09236 0.00000 0.00000 0.64010 + 6 3S -0.22177 0.52095 0.00000 0.00000 0.28053 + 7 3PX 0.00000 0.00000 0.65440 0.00000 0.00000 + 8 3PY 0.00000 0.00000 0.00000 0.30932 0.00000 + 9 3PZ -0.03739 0.08513 0.00000 0.00000 0.46101 + 10 4XX -0.00914 0.00273 0.00000 0.00000 0.01345 + 11 4YY -0.01977 0.02570 0.00000 0.00000 -0.00421 + 12 4ZZ -0.01030 0.00496 0.00000 0.00000 -0.05568 + 13 4XY 0.00000 0.00000 0.00000 0.00000 0.00000 + 14 4XZ 0.00000 0.00000 -0.04369 0.00000 0.00000 + 15 4YZ 0.00000 0.00000 0.00000 -0.05179 0.00000 + 16 2 H 1S -0.03462 0.08073 0.00000 0.23658 -0.18146 + 17 2S 0.01097 -0.02547 0.00000 0.10920 -0.09269 + 18 3 H 1S -0.03462 0.08073 0.00000 -0.23658 -0.18146 + 19 2S 0.01097 -0.02547 0.00000 -0.10920 -0.09269 + 6 7 8 9 10 + 6 3S 0.59094 + 7 3PX 0.00000 0.52394 + 8 3PY 0.00000 0.00000 0.18471 + 9 3PZ 0.22013 0.00000 0.00000 0.33273 + 10 4XX 0.00679 0.00000 0.00000 0.00971 0.00032 + 11 4YY 0.02392 0.00000 0.00000 -0.00205 0.00000 + 12 4ZZ -0.01161 0.00000 0.00000 -0.03962 -0.00111 + 13 4XY 0.00000 0.00000 0.00000 0.00000 0.00000 + 14 4XZ 0.00000 -0.03498 0.00000 0.00000 0.00000 + 15 4YZ 0.00000 0.00000 -0.03093 0.00000 0.00000 + 16 2 H 1S 0.02464 0.00000 0.14127 -0.12666 -0.00360 + 17 2S -0.05240 0.00000 0.06521 -0.06721 -0.00197 + 18 3 H 1S 0.02464 0.00000 -0.14127 -0.12666 -0.00360 + 19 2S -0.05240 0.00000 -0.06521 -0.06721 -0.00197 + 11 12 13 14 15 + 11 4YY 0.00149 + 12 4ZZ 0.00111 0.00523 + 13 4XY 0.00000 0.00000 0.00000 + 14 4XZ 0.00000 0.00000 0.00000 0.00234 + 15 4YZ 0.00000 0.00000 0.00000 0.00000 0.00518 + 16 2 H 1S 0.00694 0.01864 0.00000 0.00000 -0.02365 + 17 2S -0.00004 0.00774 0.00000 0.00000 -0.01092 + 18 3 H 1S 0.00694 0.01864 0.00000 0.00000 0.02365 + 19 2S -0.00004 0.00774 0.00000 0.00000 0.01092 + 16 17 18 19 + 16 2 H 1S 0.18268 + 17 2S 0.07353 0.03674 + 18 3 H 1S -0.03342 -0.02622 0.18268 + 19 2S -0.02622 -0.00930 0.07353 0.03674 + Full Mulliken population analysis: + 1 2 3 4 5 + 1 1 O 1S 2.07704 + 2 2S -0.04234 0.50716 + 3 2PX 0.00000 0.00000 0.81733 + 4 2PY 0.00000 0.00000 0.00000 0.51798 + 5 2PZ 0.00000 0.00000 0.00000 0.00000 0.64010 + 6 3S -0.03710 0.39782 0.00000 0.00000 0.00000 + 7 3PX 0.00000 0.00000 0.32819 0.00000 0.00000 + 8 3PY 0.00000 0.00000 0.00000 0.15513 0.00000 + 9 3PZ 0.00000 0.00000 0.00000 0.00000 0.23121 + 10 4XX -0.00031 0.00150 0.00000 0.00000 0.00000 + 11 4YY -0.00066 0.01406 0.00000 0.00000 0.00000 + 12 4ZZ -0.00035 0.00271 0.00000 0.00000 0.00000 + 13 4XY 0.00000 0.00000 0.00000 0.00000 0.00000 + 14 4XZ 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